DNA methylation (5-methylcytosine) in mammals and plants silences transposons, retroviruses, and regulates gene imprinting. In mammals, DNA hypermethylation is associated with certain diseases including the onset and progression of cancer. We discovered that the Arabidopsis DEMETER (DME) protein regulates imprinting by DNA demethylation. DME is related to DNA glycosylases that excise damaged/mispaired bases in the base excision DNA repair pathway. DME excises 5-methylcytosine that is replaced with cytosine. DME is expressed primarily in the central cell, the progenitor of the placenta-like endosperm that supports embryo development. DME demethylates and activates maternal allele expression of genes that are imprinted in the endosperm. In mammals, 88 imprinting genes have been discovered, many of which are crucial for proper embryo development. In contrast, only ten plant imprinted genes have been identified and studied in detail. To understand the genome-wide extent of DNA demethylation in the regulation of gene imprinting, we used the Illumina Genome Analyzer " to carryout high-throughput bisulfite sequencing on DNA from wild type endosperm, embryo and dme-mutant endosperm. In addition to finding several sites potentially regulated by DEMETER mediated DNA demethylation we also discovered how global DNA demethylation is invovled in trasposon silenicng.